Its got to all come together eventually!
But not necessarily in the way you think! The perfect fit, IMV but as others have hinted, comes from using the bike frequently and gently, making some adjustments to try things out and then finally making those changes permanent. I've scanned your posts briefly but I haven't discovered answers to:
1. How long have you been cycling
2. What sort of bike did you ride before your present one
3. How long have you had your knee trouble
4. What set up you used to have
5. How often you use the bike (not how many miles you do)
6. What gears you are using on which hills
I am not asking you to provide answers, I'm just saying that a comfortable fit comes from adapting yourself steadily to the bike as well as adapting the bike to you. I would say keep off high gears, walk up hills for now, keep your mileages low but your trips frequent. If you already have a target (e.g. getting to work in a specific time up certain hills etc), that may put too great a strain on your knee. You might find that all this measuring is a waste of time - there is no perfect fit while you are still getting used to things. (In the end, you might just find that the bike isn't right for you and you need a bigger one but there is quite a way to go.)
Finally I would say don't get diverted by other issues (e.g. brakes): the best bike in the world is the one you are most comfortable on - get that right first because the most technically advanced bike is next to useless if you cannot ride it.